UUP_ECOLI
ID UUP_ECOLI Reviewed; 635 AA.
AC P43672; O05662; P43673; P75865;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 168.
DE RecName: Full=ATP-binding protein Uup {ECO:0000255|HAMAP-Rule:MF_00848};
DE EC=3.6.1.- {ECO:0000255|HAMAP-Rule:MF_00848, ECO:0000269|PubMed:16407313};
GN Name=uup {ECO:0000255|HAMAP-Rule:MF_00848, ECO:0000303|PubMed:6294054};
GN Synonyms=ycbH, ycbI; OrderedLocusNames=b0949, JW0932;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-614, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9139905; DOI=10.1128/jb.179.9.2892-2899.1997;
RA Reddy M., Gowrishankar J.;
RT "Identification and characterization of ssb and uup mutants with increased
RT frequency of precise excision of transposon Tn10 derivatives: nucleotide
RT sequence of uup in Escherichia coli.";
RL J. Bacteriol. 179:2892-2899(1997).
RN [5]
RP PROTEIN SEQUENCE OF 315-320, ATPASE ACTIVITY, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION, INDUCTION, DISRUPTION
RP PHENOTYPE, DNA-BINDING, AND MUTAGENESIS OF ASP-181; ASP-465 AND
RP 551-LYS--GLY-635.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=16407313; DOI=10.1074/jbc.m509926200;
RA Murat D., Bance P., Callebaut I., Dassa E.;
RT "ATP hydrolysis is essential for the function of the Uup ATP-binding
RT cassette ATPase in precise excision of transposons.";
RL J. Biol. Chem. 281:6850-6859(2006).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 395-635.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=7751275; DOI=10.1128/jb.177.10.2673-2678.1995;
RA Koh Y.-S., Roe J.-H.;
RT "Isolation of a novel paraquat-inducible (pqi) gene regulated by the soxRS
RT locus in Escherichia coli.";
RL J. Bacteriol. 177:2673-2678(1995).
RN [7]
RP FUNCTION, AND GENETIC ANALYSIS.
RC STRAIN=K12;
RX PubMed=6294054; DOI=10.1128/jb.153.1.384-389.1983;
RA Hopkins J.D., Clements M., Syvanen M.;
RT "New class of mutations in Escherichia coli (uup) that affect precise
RT excision of insertion elements and bacteriophage Mu growth.";
RL J. Bacteriol. 153:384-389(1983).
RN [8]
RP IDENTIFICATION.
RA Rudd K.E.;
RL Unpublished observations (JUL-1995).
RN [9]
RP FUNCTION, DOMAIN, DISRUPTION PHENOTYPE, DNA-BINDING, AND MUTAGENESIS OF
RP 551-LYS--GLY-635.
RX PubMed=19948254; DOI=10.1016/j.bbapap.2009.11.017;
RA Burgos Zepeda M.Y., Alessandri K., Murat D., El Amri C., Dassa E.;
RT "C-terminal domain of the Uup ATP-binding cassette ATPase is an essential
RT folding domain that binds to DNA.";
RL Biochim. Biophys. Acta 1804:755-761(2010).
RN [10]
RP FUNCTION IN RIBOSOME ASSEMBLY, SUBCELLULAR LOCATION, INDUCTION, DISRUPTION
RP PHENOTYPE, AND MUTAGENESIS OF ASP-181; 294-GLU--GLU-300; ASP-465 AND
RP 551-LYS--GLY-635.
RC STRAIN=K12 / BW25113;
RA Cochrane K.L.;
RT "Elucidating Ribosomes-Genetic Studies of the ATPase Uup and the Ribosomal
RT Protein L1.";
RL Thesis (2015), University of Michigan, United States.
RN [11]
RP FUNCTION IN TRANSLATION, FAMILY, AND MUTAGENESIS OF GLU-182 AND GLU-466.
RC STRAIN=K12 / BW25113;
RX PubMed=30597160; DOI=10.1016/j.jmb.2018.12.013;
RA Murina V., Kasari M., Takada H., Hinnu M., Saha C.K., Grimshaw J.W.,
RA Seki T., Reith M., Putrins M., Tenson T., Strahl H., Hauryliuk V.,
RA Atkinson G.C.;
RT "ABCF ATPases involved in protein synthesis, ribosome assembly and
RT antibiotic resistance: structural and functional diversification across the
RT tree of life.";
RL J. Mol. Biol. 431:3568-3590(2019).
RN [12]
RP FUNCTION IN DNA REPAIR, DISRUPTION PHENOTYPE, AND DNA-BINDING.
RC STRAIN=K12;
RX PubMed=31665437; DOI=10.1093/nar/gkz960;
RA Romero Z.J., Armstrong T.J., Henrikus S.S., Chen S.H., Glass D.J.,
RA Ferrazzoli A.E., Wood E.A., Chitteni-Pattu S., van Oijen A.M., Lovett S.T.,
RA Robinson A., Cox M.M.;
RT "Frequent template switching in postreplication gaps: suppression of
RT deleterious consequences by the Escherichia coli Uup and RadD proteins.";
RL Nucleic Acids Res. 48:212-230(2020).
RN [13] {ECO:0007744|PDB:2LW1}
RP STRUCTURE BY NMR OF 528-635, AND COILED COIL.
RC STRAIN=K12;
RX PubMed=22995754; DOI=10.1016/j.jsb.2012.09.005;
RA Carlier L., Haase A.S., Burgos Zepeda M.Y., Dassa E., Lequin O.;
RT "The C-terminal domain of the Uup protein is a DNA-binding coiled coil
RT motif.";
RL J. Struct. Biol. 180:577-584(2012).
CC -!- FUNCTION: Probably plays a role in ribosome assembly or function;
CC overexpression suppresses cold-sensitive growth of a bipA deletion
CC (Ref.10) (Probable). May be involved in resolution of branched DNA
CC intermediates that result from template switching in postreplication
CC gaps. Binds DNA at Holliday junctions. May be involved in the correct
CC segregation of nucleoids (PubMed:31665437). Has ATPase activity, binds
CC DNA non-sequence specifically; the presence of DNA does not change the
CC ATPase activity (PubMed:16407313). Mutations in this gene cause an
CC increase in RecA-independent precise excision of transposons and
CC insertion elements, and also reduce bacteriophage Mu growth
CC (PubMed:6294054, PubMed:16407313, PubMed:19948254).
CC {ECO:0000269|PubMed:16407313, ECO:0000269|PubMed:19948254,
CC ECO:0000269|PubMed:31665437, ECO:0000269|PubMed:6294054,
CC ECO:0000269|Ref.10, ECO:0000305|PubMed:30597160}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00848, ECO:0000269|PubMed:16407313};
CC -!- ACTIVITY REGULATION: ATPase activity inhibited by N-ethylmaleimide but
CC not by vanadate. {ECO:0000269|PubMed:16407313}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.35 mM for ATP {ECO:0000269|PubMed:16407313};
CC Vmax=26 nmol/min/mg enzyme {ECO:0000269|PubMed:16407313};
CC -!- INTERACTION:
CC P43672; P0A8N3: lysS; NbExp=2; IntAct=EBI-559429, EBI-552719;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00848,
CC ECO:0000269|PubMed:16407313, ECO:0000269|Ref.10}. Note=Associates with
CC ribosomes. {ECO:0000255|HAMAP-Rule:MF_00848, ECO:0000269|Ref.10}.
CC -!- INDUCTION: Present from early exponential to stationary phase in equal
CC amounts (at protein level). {ECO:0000269|PubMed:16407313,
CC ECO:0000269|Ref.10}.
CC -!- DOMAIN: The C-terminal domain (CTD) helps bind DNA, is required to
CC complement a gene deletion. {ECO:0000269|PubMed:19948254}.
CC -!- DISRUPTION PHENOTYPE: Increase in the frequency of precise transposon
CC excision (PubMed:9139905, PubMed:16407313, PubMed:19948254). No visible
CC growth phenotype at 37 or 18 degrees Celsius. A double bipA-uup
CC deletion does not grow at 18 degrees Celsius, i.e. the uup deletion
CC exacerbates the bipA deletion (Ref.10). Deletion leads to an increase
CC in DNA crossing over, DNA repeat deletion and DNA repeat expansion;
CC double uup-radD deletion increases the phenotypes. Although single uup
CC deleted cells replicate normally, they are filamentous and lack defined
CC nucleoids, again exacerbated by a radD deletion (PubMed:31665437).
CC {ECO:0000269|PubMed:16407313, ECO:0000269|PubMed:19948254,
CC ECO:0000269|PubMed:31665437, ECO:0000269|PubMed:9139905,
CC ECO:0000269|Ref.10}.
CC -!- SIMILARITY: Belongs to the ABC transporter superfamily. ABCF family.
CC Uup subfamily. {ECO:0000255|HAMAP-Rule:MF_00848,
CC ECO:0000303|PubMed:30597160}.
CC -!- SEQUENCE CAUTION:
CC Sequence=X81561; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; U00096; AAC74035.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35707.1; -; Genomic_DNA.
DR EMBL; Y09439; CAA70589.1; -; Genomic_DNA.
DR EMBL; X81561; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; D64835; D64835.
DR RefSeq; NP_415469.1; NC_000913.3.
DR RefSeq; WP_000053099.1; NZ_SSZK01000002.1.
DR PDB; 2LW1; NMR; -; A=528-635.
DR PDBsum; 2LW1; -.
DR AlphaFoldDB; P43672; -.
DR BMRB; P43672; -.
DR SMR; P43672; -.
DR BioGRID; 4260026; 20.
DR DIP; DIP-11099N; -.
DR IntAct; P43672; 13.
DR STRING; 511145.b0949; -.
DR TCDB; 3.A.1.120.6; the atp-binding cassette (abc) superfamily.
DR jPOST; P43672; -.
DR PaxDb; P43672; -.
DR PRIDE; P43672; -.
DR EnsemblBacteria; AAC74035; AAC74035; b0949.
DR EnsemblBacteria; BAA35707; BAA35707; BAA35707.
DR GeneID; 945566; -.
DR KEGG; ecj:JW0932; -.
DR KEGG; eco:b0949; -.
DR PATRIC; fig|1411691.4.peg.1325; -.
DR EchoBASE; EB2933; -.
DR eggNOG; COG0488; Bacteria.
DR HOGENOM; CLU_000604_36_0_6; -.
DR InParanoid; P43672; -.
DR OMA; AQADKMR; -.
DR PhylomeDB; P43672; -.
DR BioCyc; EcoCyc:UUP-MON; -.
DR PRO; PR:P43672; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:EcoCyc.
DR GO; GO:0005886; C:plasma membrane; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IBA:GO_Central.
DR GO; GO:0016887; F:ATP hydrolysis activity; IDA:EcoCyc.
DR GO; GO:0003677; F:DNA binding; IDA:EcoCyc.
DR GO; GO:0043022; F:ribosome binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006301; P:postreplication repair; IMP:EcoCyc.
DR GO; GO:0070894; P:regulation of transposon integration; IMP:EcoCyc.
DR GO; GO:0009314; P:response to radiation; IMP:EcoCyc.
DR Gene3D; 1.10.287.380; -; 1.
DR Gene3D; 3.40.50.300; -; 2.
DR HAMAP; MF_00848; Uup; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR032524; ABC_tran_C.
DR InterPro; IPR032781; ABC_tran_Xtn.
DR InterPro; IPR003439; ABC_transporter-like_ATP-bd.
DR InterPro; IPR017871; ABC_transporter-like_CS.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR043686; Uup.
DR InterPro; IPR037118; Val-tRNA_synth_C_sf.
DR Pfam; PF00005; ABC_tran; 2.
DR Pfam; PF16326; ABC_tran_CTD; 1.
DR Pfam; PF12848; ABC_tran_Xtn; 1.
DR SMART; SM00382; AAA; 2.
DR SUPFAM; SSF52540; SSF52540; 2.
DR PROSITE; PS00211; ABC_TRANSPORTER_1; 2.
DR PROSITE; PS50893; ABC_TRANSPORTER_2; 2.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Coiled coil; Cytoplasm;
KW Direct protein sequencing; DNA damage; DNA repair; DNA-binding; Hydrolase;
KW Nucleotide-binding; Reference proteome; Repeat.
FT CHAIN 1..635
FT /note="ATP-binding protein Uup"
FT /id="PRO_0000093029"
FT DOMAIN 1..253
FT /note="ABC transporter 1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00848"
FT DOMAIN 320..546
FT /note="ABC transporter 2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00848"
FT REGION 551..635
FT /note="C-terminal domain (CTD), binds DNA, required to
FT complement a deletion mutant"
FT /evidence="ECO:0000269|PubMed:19948254"
FT COILED 563..631
FT /evidence="ECO:0000269|PubMed:22995754,
FT ECO:0007744|PDB:2LW1"
FT BINDING 36..43
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00848"
FT BINDING 352..359
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00848"
FT MUTAGEN 181
FT /note="D->N: No longer hydrolyzes ATP, has a high level of
FT transposon excision. No growth change at 37 or 18 degrees
FT Celsius, not required to suppress bipA deletion."
FT /evidence="ECO:0000269|PubMed:16407313, ECO:0000269|Ref.10"
FT MUTAGEN 182
FT /note="E->Q: Causes growth defect at 37 degrees Celsius, 6-
FT fold decrease in translation; when associated with Q-464
FT (called EQ2)."
FT /evidence="ECO:0000269|PubMed:30597160"
FT MUTAGEN 294..300
FT /note="Missing: Decreases growth at 18 degrees Celsius,
FT does not suppress bipA deletion in cold, stronger
FT association with ribosomes."
FT /evidence="ECO:0000269|Ref.10"
FT MUTAGEN 465
FT /note="D->N: No longer hydrolyzes ATP, has a high level of
FT transposon excision. Inhibits growth at 37 and 18 degrees
FT Celsius, does not suppress bipA deletion in cold, stronger
FT association with ribosomes."
FT /evidence="ECO:0000269|PubMed:16407313, ECO:0000269|Ref.10"
FT MUTAGEN 466
FT /note="E->Q: Causes growth defect at 37 degrees Celsius, 6-
FT fold decrease in translation; when associated with Q-181
FT (EQ2)."
FT /evidence="ECO:0000269|PubMed:30597160"
FT MUTAGEN 551..635
FT /note="Missing: Reduces DNA binding 2-fold, no change in
FT ATP hydrolysis, has a high level of transposon excision. No
FT growth change at 37 or 18 degrees Celsius, does not
FT suppress bipA deletion in cold, stronger association with
FT ribosomes."
FT /evidence="ECO:0000269|PubMed:16407313,
FT ECO:0000269|PubMed:19948254, ECO:0000269|Ref.10"
FT STRAND 556..559
FT /evidence="ECO:0007829|PDB:2LW1"
FT HELIX 564..592
FT /evidence="ECO:0007829|PDB:2LW1"
FT HELIX 596..598
FT /evidence="ECO:0007829|PDB:2LW1"
FT HELIX 601..633
FT /evidence="ECO:0007829|PDB:2LW1"
SQ SEQUENCE 635 AA; 72067 MW; B1EAC2086BE193D2 CRC64;
MSLISMHGAW LSFSDAPLLD NAELHIEDNE RVCLVGRNGA GKSTLMKILN REQGLDDGRI
IYEQDLIVAR LQQDPPRNVE GSVYDFVAEG IEEQAEYLKR YHDISRLVMN DPSEKNLNEL
AKVQEQLDHH NLWQLENRIN EVLAQLGLDP NVALSSLSGG WLRKAALGRA LVSNPRVLLL
DEPTNHLDIE TIDWLEGFLK TFNGTIIFIS HDRSFIRNMA TRIVDLDRGK LVTYPGNYDQ
YLLEKEEALR VEELQNAEFD RKLAQEEVWI RQGIKARRTR NEGRVRALKA MRRERGERRE
VMGTAKMQVE EASRSGKIVF EMEDVCYQVN GKQLVKDFSA QVLRGDKIAL IGPNGCGKTT
LLKLMLGQLQ ADSGRIHVGT KLEVAYFDQH RAELDPDKTV MDNLAEGKQE VMVNGKPRHV
LGYLQDFLFH PKRAMTPVRA LSGGERNRLL LARLFLKPSN LLILDEPTND LDVETLELLE
ELIDSYQGTV LLVSHDRQFV DNTVTECWIF EGGGKIGRYV GGYHDARGQQ EQYVALKQPA
VKKTEEAAAA KAETVKRSSS KLSYKLQREL EQLPQLLEDL EAKLEALQTQ VADASFFSQP
HEQTQKVLAD MAAAEQELEQ AFERWEYLEA LKNGG
